Background: Approximately 80% of patients with indwelling ureteral stents experience stent related symptoms (SRS). We believe SRS can be reduced through altering the composition of ureteral stents to a less firm material. Therefore, we aim to compare modern silicone and polyurethane ureteral stents in terms of SRS intensity and safety. Methods: From June 2018 to October 2018, patients from two distinct clinical centers were prospectively enrolled in the study and stratified (non-randomly) into either control group A, patients who received polyurethane stents (Rüsch, Teleflex), or experimental group B, patients who received silicone stents (Cook Medical). Each participant completed a survey 1 h after stent insertion, in the middle of the stent dwelling period, and before stent removal or ureteroscopy noting body pain and overactive bladder via the visual analog scale pain (VASP) and overactive bladder (OAB) awareness tool, respectively. Additionally, successfulness of stent placement, hematuria, number of unplanned visits, and stent encrustation rates were assessed within each group. Results: A total of 50 patients participated in the study, control group A consisted of 20 patients and experimental group B consisted of 30 patients. Participants in group B, silicone ureteral stents, demonstrated significantly lower mean values of VASP 2 weeks prior to stent removal and promptly before stent removal (p = 0.023 and p = 0.014, respectively). No other comparisons between the two groups were statistically significant. Conclusions: Compared to polyurethane ureteral stents, silicone ureteral stents are associated with lower body pain intensity assessed by VASP 2 weeks before stent removal and at the time of stent removal. Trial registration: Current Controlled Trials NCT04000178. Retrospectively registered on June 26, 2019.